Umakhanth Venkatraman Girija

Dr Umakhanth Venkatraman Girija

Job: Senior Lecturer (VC2020) and Programme Leader for MSc Advanced Biomedical Science

Faculty: Health and Life Sciences

School/department: School of Allied Health Sciences

Address: 51漫画, The Gateway, Leicester, LE1 9BH

T: +44(0) 116 2577717

E: umakhanth.venkatramangirija@dmu.ac.uk

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Personal profile

Dr Umakhanth Venkatraman Girija is a lecturer in Immunology in the School of Allied health Sciences, 51漫画. He completed his PhD in Biochemistry from University of Oxford.

During his doctoral research, Umakhanth investigated the protein-protein interactions leading to the lectin pathway of complement activation, an important component of innate immune system. His postdoctoral work with University of Leicester expanded his interest into the molecular mechanism of classical pathway of complement activation and also on the role of lectins in immunity.

In addition to academic research, Umakhanth has six years of industrial research experience from Biocon, India, where he developed company’s first GMO producing recombinant therapeutic which is in market. He was a team leader for various molecular biology projects which were done in collaboration with multinational pharma companies from Europe and USA.

Currently, Umakhanth's research focuses on how microbial pathogens evade host complement attack and also on the role of adiponectins which has important cardio protective function. He has research collaborations with Universities of Leicester, Brunel and Warwick.

Research group affiliations

Biomedical and Environmental Health Group
Infectious Disease Research Group

Publications and outputs

dc.title: Interactions of Candida tropicalis pH-related antigen 1 with Complement Proteins C3, C3b, factor-H, C4BP and Complement Evasion dc.contributor.author: Valand, Nisha; Gazioglu, Ozcan; Yesilkaya, Hasan; Shivkumar, Maitreyi; Horley, Neill; Arroo, R. R. J.; Wallis, Russell; Kishore, Uday; Venkatraman Girija, U. dc.description.abstract: Candida, as a part of the human microbiota, can cause opportunistic infections that are either localised or systemic candidiasis. Emerging resistance to the standard antifungal drugs is associated with increased mortality rate due to invasive Candida infections, particularly in immunocompromised patients. While there are several species of Candida, an increasing number of Candida tropicalis isolates have been recently reported from patients with invasive candidiasis or inflammatory bowel diseases. In order to establish infections, C. tropicalis has to adopt several strategies to escape the host immune attack. Understanding the immune evasion strategies is of great importance as these can be exploited as novel therapeutic targets. C. albicans pH-related antigen 1 (CaPra1), a surface bound and secretory protein, has been found to interact strongly with the immune system and help in complement evasion. However, the role of C. tropicalis Pra1 (CtPra1) and its interaction with the complement is not studied yet. Thus, we characterised how pH-related antigen 1 of C. tropicalis (CtPra1) interacts with some of the key complement proteins of the innate immune system. CtPra1 was recombinantly produced using a Kluyveromyces lactis yeast expression system. Recombinant CtPra1, was found to bind human C3 and C3b, central molecules of the complement pathways that are important components of the innate immune system. It was also found to bind human complement regulatory proteins factor-H and C4b-binding protein (C4BP). CtPra1-factor-H and CtPra1-C4BP interactions were found to be ionic in nature as the binding intensity affected by high sodium chloride concentrations. CtPra1 inhibited functional complement activation with different effects on classical (鈭�20 %), lectin (鈭�25 %) and alternative (鈭�30 %) pathways. qPCR experiments using C. tropicalis clinical isolates (oral, blood and peritoneal fluid) revealed relatively higher levels of expression of CtPra1 gene when compared to the reference strain. Native CtPra1 was found to be expressed both as membrane-bound and secretory forms in the clinical isolates. Thus, C. tropicalis appears to be a master of immune evasion by using Pra1 protein. Further investigation using in-vivo models will help ascertain if these proteins can be novel therapeutic targets. dc.description: The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.
dc.title: Inactivation of the Complement Lectin Pathway by Candida tropicalis Secreted Aspartyl Protease-1 dc.contributor.author: Valand, Nisha; Brunt, Emily; Gazioglu, Ozcan; Yesilkaya, Hasan; Mitchell, Daniel; Horley, Neill; Arroo, R. R. J.; Kishore, Uday; Wallis, Russell; Venkatraman Girija, U. dc.description.abstract: Candida tropicalis is an opportunistic fungal pathogen and is one of the most frequently isolated non-albicans species. It can cause localised as well as invasive systemic infections particularly in immunocompromised patients. Increased resistance to common anti-fungal drugs is an emerging problem. In order to establish disseminated infections, Candida has evolved several strategies to escape the host immune system. A detailed understanding of how C. tropicalis escapes the host immune attack is needed as it can help develop novel anti-fungal therapies. Secreted aspartyl proteinases (Saps) of C. albicans have been shown to be determinants of virulence and immune evasion. However, the immune evasion properties of C. tropicalis Saps have been poorly characterised. This study investigated the immune evasion properties of C. tropicalis secreted aspartic protease 1 (Sapt1). Sapt1 was recombinantly produced using a Kluyveromyces lactis yeast expression system. A range of complement proteins and immunogloublins were screened to test if Sapt1 had any proteolytic activity. Sapt1 efficiently cleaved human mannose-binding lectin (MBL) and collectin-11, which are the initiating molecules of the lectin pathway of the complement system, but not l-ficolin. In addition, Sapt1 cleaved DC-SIGN, the receptor on antigen presenting dendritic cells. Proteolysis was prominent in acidic condition (pH 5.2), a characteristic of aspartyl protease. No proteolytic activity was detected against complement proteins C1q, C3, C3b, IgG and IgA. In view of the ability of Sapt1 to cleave MBL and collectin-11, we found that Sapt1 could prevent activation of the complement lectin pathway. RT-qPCR analysis using three different C. tropicalis clinical isolates (oral, blood and peritoneal dialysis fluid) revealed relatively higher levels of mRNA expression of Sapt1 gene when compared to a reference strain; Sapt1 protein was found to be secreted by all the tested strains. Lectin pathway and its initiating components are crucial to provide front line defence against Candida infections. For the first time, we have shown that a Candida protease can proteolytically degrade the key initiating components of lectin pathway and inhibit complement activation. Findings from this study highlight the importance of exploring Sapt1 as a potential therapeutic target. We conclude that C. tropicalis secretes Sapt1 to target the complement lectin pathway, a key pattern recognition and clearance mechanism, for its survival and pathogenesis. dc.description: open access article
dc.title: Candida Pathogenicity and Interplay with the Immune System dc.contributor.author: Valand, Nisha; Venkatraman Girija, U. dc.description.abstract: Candida species are opportunistic fungal pathogens that are part of the normal skin and mucosal microflora. Overgrowth of Candida can cause infections such as thrush or life-threatening invasive candidiasis in immunocompromised patients. Though Candida albicans is highly prevalent, several non-albicans species are also isolated from nosocomial infections. Candida sp. are over presented in the gut of people with Crohn鈥檚 disease and certain types of neurological disorders, with hyphal form and biofilms being the most virulent states. In addition, Candida uses several secreted and cell surface molecules such as pH related antigen 1, High affinity glucose transporter, Phosphoglycerate mutase 1 and lipases to establish pathogenicity. A strong innate immune response is elicited against Candida via dendritic cells, neutrophils and macrophages. All three complement pathways are also activated. Production of proinflammatory cytokines IL-10 and IL-12 signal differentiation of CD4+ cells into Th1 and Th2 cells, whereas IL-6, IL-17 and IL-23 induce Th17 cells. Importance of T-lymphocytes is reflected in depleted T-cell count patients being more prone to Candidiasis. Anti- Candida antibodies also play a role against candidiasis using various mechanisms such as targeting virulent enzymes and exhibiting direct candidacidal activity. However, the significance of antibody response during infection remains controversial. Furthermore, some of the Candida strains have evolved molecular strategies to evade the sophisticated host attack by proteolysis of components of immune system and interfering with immune signalling pathways. Emergence of several non-albicans species that are resistant to current antifungal agents makes treatment more difficult. Therefore, deeper insight into interactions between Candida and the host immune system is required for discovery of novel therapeutic options.
dc.title: A hybrid ligand and structure-based virtual screening of NCI compound library identifies potential SAPT1 inhibitors dc.contributor.author: Sari, Suat; Valand, Nisha; Venkatraman Girija, U. dc.description.abstract: Secretory aspartate proteases (SAPs) is a key virulence factor of Candida spp. enabling adherence to and invasion of host tissues through breakdown of host proteins related to immunological and structural defenses, making them potential drug targets for drug-resistant mycoses, especially where the available therapies fail. To date, no SAP inhibitors for Candida tropicalis, one of the top five most common species isolated in Candida-related mycoses, has been reported. In this study, we report first-time identification of a set of potential C. tropicalis SAP1 (SAPT1) inhibitors through a hybrid ligand-and structure-based virtual screening of National Cancer Institute (NCI) library compounds. The NCI library was refined by filtering off non-druglike molecules. Referring to a known C. albicans SAP inhibitor, a similarity search was performed for the refined library, in addition to a pharmacophore screen using a model of the ligand-receptor interactions between a peptide substrate and SAPT1 obtained from crystallographic data. The compounds selected from these screens were subject to molecular docking to the SAPT1 active site and the top-scoring ligand-receptor complexes were further included in MM-GBSA calculations to optimize the predicted binding affinities. Finally, the selected 16 compounds, which were confirmed to make key interactions with the catalytic residues, were in silico evaluated and found eligible for certain pharmacokinetic properties. As a future prospect, obtaining these virtual hits and testing them in vitro against SAPT1 could validate the virtual screening process and yield the first small molecule inhibitors of SAPT. dc.description: open access article
dc.title: Structure-function analysis for the development of peptide inhibitors for a Gram-positive quorum sensing system dc.contributor.author: Abdullah, Iman Tajer; Ulijasz, Andrew; Venkatraman Girija, U.; Tam, Sien; Andrew, Peter; Luisa Hiller, Natalia; Wallis, Russell; Yesilkaya, Hasan dc.description.abstract: The Streptococcus pneumoniae Rgg144/SHP144 regulator-peptide quorum sensing (QS) system is critical for nutrient utilization, oxidative stress response, and virulence. Here, we characterized this system by assessing the importance of each residue within the active short hydrophobic peptide (SHP) by alanine-scanning mutagenesis and testing the resulting peptides for receptor binding and activation of the receptor. Interestingly, several of the mutations had little effect on binding to Rgg144 but reduced transcriptional activation appreciably. In particular, a proline substitution (P21A) reduced transcriptional activation by 29-fold but bound with a 3-fold higher affinity than the wild-type SHP. Consistent with the function of Rgg144, the mutant peptide led to decreased utilization of mannose and increased susceptibility to superoxide generator paraquat. Pangenome comparison showed full conservation of P21 across SHP144 allelic variants. Crystallization of Rgg144 in the absence of peptide revealed a comparable structure to the DNA bound and free forms of its homologs suggesting similar mechanisms of activation. Together, these analyses identify key interactions in a critical pneumococcal QS system. Further manipulation of the SHP has the potential to facilitate the development of inhibitors that are functional across strains. The approach described here is likely to be effective across QS systems in multiple species. dc.description: open access article
dc.title: Heme binding to human CLOCK affects interactions with the E-box dc.contributor.author: Freeman, S.L.; Kwon, H.; Portolano, N.; Parkin, G.; Venkatraman Girija, U.; Basran, J.; Fielding, A.; Fairall, L.; Svistunenko, D.; Moody, P.; Schwabe, J.; Kyriacou, C.; Raven, E. dc.description.abstract: The circadian clock is an endogenous time-keeping system that is ubiquitous in animals and plants as well as some bacteria. In mammals, the clock regulates the sleep-wake cycle via 2 basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) domain proteins-CLOCK and BMAL1. There is emerging evidence to suggest that heme affects circadian control, through binding of heme to various circadian proteins, but the mechanisms of regulation are largely unknown. In this work we examine the interaction of heme with human CLOCK (hCLOCK). We present a crystal structure for the PAS-A domain of hCLOCK, and we examine heme binding to the PAS-A and PAS-B domains. UV-visible and electron paramagnetic resonance spectroscopies are consistent with a bis-histidine ligated heme species in solution in the oxidized (ferric) PAS-A protein, and by mutagenesis we identify His144 as a ligand to the heme. There is evidence for flexibility in the heme pocket, which may give rise to an additional Cys axial ligand at 20K (His/Cys coordination). Using DNA binding assays, we demonstrate that heme disrupts binding of CLOCK to its E-box DNA target. Evidence is presented for a conformationally mobile protein framework, which is linked to changes in heme ligation and which has the capacity to affect binding to the E-box. Within the hCLOCK structural framework, this would provide a mechanism for heme-dependent transcriptional regulation. dc.description: The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.
dc.title: Structure of the C1r-C1s interaction of the C1 complex of complement activation dc.contributor.author: Almitairi, J.O.M.; Venkatraman Girija, U.; Furze, Christopher M.; Simpson-Gray, X.; Badakshi, F.; Marshall, Jamie E.; Schwaeble, W. J.; Mitchell, D. A.; Moody, P. C. E.; Wallis, R. dc.description.abstract: The multiprotein complex C1 initiates the classical pathway of complement activation on binding to antibody鈥揳ntigen complexes, pathogen surfaces, apoptotic cells, and polyanionic structures. It is formed from the recognition subcomponent C1q and a tetramer of proteases C1r2C1s2 as a Ca2+-dependent complex. Here we have determined the structure of a complex between the CUB1-EGF-CUB2 fragments of C1r and C1s to reveal the C1r鈥� C1s interaction that forms the core of C1. Both fragments are Lshaped and interlock to form a compact antiparallel heterodimer with a Ca2+ from each subcomponent at the interface. Contacts, involving all three domains of each protease, are more extensive than those of C1r or C1s homodimers, explaining why heterocomplexes form preferentially. The available structural and biophysical data support a model of C1r2C1s2 in which two C1r-C1s dimers are linked via the catalytic domains of C1r. They are incompatible with a recent model in which the N-terminal domains of C1r and C1s form a fixed tetramer. On binding to C1q, the proteases become more compact, with the C1r-C1s dimers at the center and the six collagenous stems of C1q arranged around the perimeter. Activation is likely driven by separation of the C1r-C1s dimer pairs when C1q binds to a surface. Considerable flexibility in C1s likely facilitates C1 complex formation, activation of C1s by C1r, and binding and activation of downstream substrates C4 and C4b-bound C2 to initiate the reaction cascade. dc.description: The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.
dc.title: Molecular basis of sugar recognition by collectin-K1 and the effects of mutations associated with 3MC syndrome dc.contributor.author: Furze, Christopher M.; Gingras, Alexandre R.; Yoshizaki, Takayuki; Ohtani, Katsuki; Marshall, Jamie E.; Wallis, A. K.; Schwaeble, W. J.; El-Mezgueldi, Mohammed; Mitchell, D. A.; Moody, P. C. E.; Wakamiya, Nobutaka; Wallis, R.; Venkatraman Girija, U. dc.description.abstract: BACKGROUND: Collectin-K1 (CL-K1, or CL-11) is a multifunctional Ca(2+)-dependent lectin with roles in innate immunity, apoptosis and embryogenesis. It binds to carbohydrates on pathogens to activate the lectin pathway of complement and together with its associated serine protease MASP-3 serves as a guidance cue for neural crest development. High serum levels are associated with disseminated intravascular coagulation, where spontaneous clotting can lead to multiple organ failure. Autosomal mutations in the CL-K1 or MASP-3 genes cause a developmental disorder called 3MC (Carnevale, Mingarelli, Malpuech and Michels) syndrome, characterised by facial, genital, renal and limb abnormalities. One of these mutations (Gly(204)Ser in the CL-K1 gene) is associated with undetectable levels of protein in the serum of affected individuals. RESULTS: In this study, we show that CL-K1 primarily targets a subset of high-mannose oligosaccharides present on both self- and non-self structures, and provide the structural basis for its ligand specificity. We also demonstrate that three disease-associated mutations prevent secretion of CL-K1 from mammalian cells, accounting for the protein deficiency observed in patients. Interestingly, none of the mutations prevent folding or oligomerization of recombinant fragments containing the mutations in vitro. Instead, they prevent Ca(2+) binding by the carbohydrate-recognition domains of CL-K1. We propose that failure to bind Ca(2+) during biosynthesis leads to structural defects that prevent secretion of CL-K1, thus providing a molecular explanation of the genetic disorder. CONCLUSIONS: We have established the sugar specificity of CL-K1 and demonstrated that it targets high-mannose oligosaccharides on self- and non-self structures via an extended binding site which recognises the terminal two mannose residues of the carbohydrate ligand. We have also shown that mutations associated with a rare developmental disorder called 3MC syndrome prevent the secretion of CL-K1, probably as a result of structural defects caused by disruption of Ca(2+) binding during biosynthesis.
dc.title: Analogous Interactions in Initiating Complexes of the Classical and Lectin Pathways of Complement dc.contributor.author: Phillips, A. E.; Toth, J.; Dodds, A. W.; Venkatraman Girija, U.; Furze, Christopher M.; Pala, E.; Sim, R.B.; Reid, K. B. M.; Schwaeble, W. J.; Schmid, R.; Keeble, A. H.; Wallis, R. dc.description.abstract: The classical and lectin pathways of complement activation neutralize pathogens and stimulate key immunological processes. Both pathways are initiated by collagen-containing, soluble pattern recognition molecules associated with specific serine proteases. In the classical pathway, C1q binds to Ab-Ag complexes or bacterial surfaces to activate C1r and C1s. In the lectin pathway, mannan-binding lectin and ficolins bind to carbohydrates on pathogens to activate mannan-binding lectin-associated serine protease 2. To characterize the interactions leading to classical pathway activation, we have analyzed binding between human C1q, C1r, and C1s, which associate to form C1, using full-length and truncated protease components. We show that C1r and C1s bind to C1q independently. The CUB1-epidermal growth factor fragments contribute most toward binding, but CUB2 of C1r, but not of C1s, is also important. Each C1rs tetramer presents a total of six binding sites, one for each of the collagenous domains of C1q. We also demonstrate that subcomponents of the lectin and classical pathways cross-interact. Thus, although the stoichiometries of complexes differ, interactions are analogous, with equivalent contacts between recognition and protease subcomponents. Importantly, these new data are contrary to existing models of C1 and enable us to propose a new model using mannan-binding lectin-mannan-binding lectin-associated serine protease interactions as a template.
dc.title: Engineering novel complement activity into a pulmonary-surfactant protein dc.contributor.author: Venkatraman Girija, U.; Furze, C.; Toth, J.; Schwaeble, W. J.; Mitchell, D. A.; Keeble, A. H.; Wallis, R. dc.description.abstract: Complement neutralizes invading pathogens, stimulates inflammatory and adaptive immune responses, and targets non- or altered-self structures for clearance. In the classical and lectin activation pathways, it is initiated when complexes composed of separate recognition and activation subcomponents bind to a pathogen surface. Despite its apparent complexity, recognition-mediated activation has evolved independently in three separate protein families, C1q, mannose-binding lectins (MBLs), and serum ficolins. Although unrelated, all have bouquet-like architectures and associate with complement-specific serine proteases: MBLs and ficolins with MBL-associated serine protease-2 (MASP-2) and C1q with C1r and C1s. To examine the structural requirements for complement activation, we have created a number of novel recombinant rat MBLs in which the position and orientation of the MASP-binding sites have been changed. We have also engineered MASP binding into a pulmonary surfactant protein (SP-A), which has the same domain structure and architecture as MBL but lacks any intrinsic complement activity. The data reveal that complement activity is remarkably tolerant to changes in the size and orientation of the collagenous stalks of MBL, implying considerable rotational and conformational flexibility in unbound MBL. Furthermore, novel complement activity is introduced concurrently with MASP binding in SP-A but is uncontrolled and occurs even in the absence of a carbohydrate target. Thus, the active rather than the zymogen state is default in lectin.MASP complexes and must be inhibited through additional regions in circulating MBLs until triggered by pathogen recognition.

Research interests/expertise

Innate Immune System and complement pathways
Microbial pathogens and immune evasion strategies
Applied Biotechnology (recombinant protein expression)
Microbial strain engineering

Main techniques used in the laboratory include gene cloning, site-directed mutagenesis, recombinant protein expression in various host systems, protein purification, protein-protein interactions, assay development, cell culture and molecular microbiology (e.g. gene knockouts).

Areas of teaching

Immunology
Microbiology
Molecular Biology
Applied Biotechnology

Qualifications

PhD Biochemistry (University of Oxford)
MSc Microbiology (India)
PGCertHE (51漫画)

Courses taught

BSc (Hons) Biomedical Science
BSc Medical Science
MSc Advanced Biomedical Science

Honours and awards

Best Poster Award, Complement UK meeting, New Castle, UK (October 2013)
Overseas Research Scholarship award for Doctoral study at University of Oxford (2006-08)
Biocontribute award in the industry for developing company’s first GMO and for successful collaborative research with pharma clients (December 2002 and December 2003)
Gold Medal for securing University First Rank in graduate studies in Microbiology (June1997 and June 1999)

Membership of external committees

Review Editor, the Editorial Board of Molecular Innate Immunity, a specialty of Frontiers in Immunology (since Nov 2015).

Conference attendance

4th Complement UK meeting, Leicester, UK, November 2016
11th International Conference on Innate Immunity, Olympia, Greece, June 2014
Complement UK meeting, New Castle, UK, October 2013
XII International Complement Workshop, Basel, Switzerland, October 2008
International Complement Meeting, MRC Immunochemistry Unit, Oxford, UK; July 2008
XI European meeting on Complement in Human Disease, Cardiff, UK; September, 2007
VI International Workshop on C1 and the Collectins, Seeheim, Germany; June 2006

Current research students

Miss Nisha Valand (PhD student, 1^st supervisor; Topic: Molecular immune evasion strategies of Candida tropicalis; Oct 2017 -)
Miss Emily Brunt (MSc research, Molecular Immunology, 1^st supervisor; Oct 2017 -)
Mr Medhanie Habtom (MSc research, Molecular Immunology, 1^st supervisor; Oct 2017 - )

Internally funded research project information

Project title: Schistosomiasis: Molecular investigation towards novel drug target and vaccine design

Value: £6959

Funding source: RIF7 (Research Investment Fund)

Start date: August 2015

End date: July 2016

Role in project: Principal Investigator

Project title: Protein Production Facility

Value: £46942

Funding source: RCIF2 (Research Capital Investment Funding 2)

Start date: December 2015

End date: July 2016

Role in project: Principal Investigator

Project title: Molecular characterization and identification of emerging parasitic pathogens in the environment in the midlands UK: Public health implications

Value: £21768

Funding source: RCIF2 (Research Capital Investment Funding 2)

Start date: December 2015

End date: July 2016

Role in project: Co-applicant (PI: Dr A Peña Fernández)

Project title: Coulter Counter and Cytospin

Value: £22494

Funding source: Capital bid

Start date: July 2016

Role in project: Co-applicant (PI: Dr Neenu Singh)