LAKSHMINARAYAN  M. IYER

 

 

National Center for Biotechnology Information,

National Institutes of Health,

Bethesda, Maryland, 20894, USA.

Email: lakshmin at mail dot nih dot gov

Education

 

Ph.D., Biology, Department of Biology, Texas A&M University, College Station, TX, USA. 1993-1999. Dissertation title: Post-transcriptional gene silencing of RNA‑2 in Brome mosaic virus 

           Advisor:  Dr. Timothy. C. Hall.

 

M.S., Biotechnology, Department of Biotechnology, Madurai Kamaraj University, Madurai, India. 1991-1993.

            Thesis title : Molecular modelling of the E. coli endonuclease McrA. 

            Advisor: Dr. S Krishnaswamy.

 

B.S., Microbiology, Department of Microbiology, Ramnarain Ruia College, University of Bombay, Mumbai, India. 1988-1991.

 

Professional Experience

 

Staff Scientist, August 2005-

Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.

 

Visiting Postdoctoral Research Fellow, August 2000 – August 2005

Dr. Eugene Koonin’s group, Computational Biology Branch, National Center for Biotechnology Information, National Institutes  of Health, Bethesda, MD, USA.

 

Postdoctoral Research Associate, Jan 2000 – June 2000.

Dr. Timothy Hall’s Laboratory, Institute of Developmental and Molecular Biology,  Department of Biology, Texas A&M University, College Station, TX, USA. 

 

Graduate Research Assistant, 1994-95, 1998.

Dr. Timothy Hall’s Laboratory, Institute of Developmental and Molecular Biology,  Department of Biology, Texas A&M University, College Station, TX, USA. 

 

Graduate Teaching Assistant, 1993- 94, 1996-97, Fall 1999.

Department of Biology, Texas A&M University, College Station, TX, USA.

 

 

Summer-Internship, 1992.

Hindustan Lever Research Center (a subsidiary of Unilever), Chakala, Mumbai, India.

 

Honors

 

Outstanding Graduate Student Teacher Award, Department of Biology, Texas A&M University, 1999.

 

Peer Reviewed Publications

 

1.      Velikovsky. C.A., Deng, L., Tasumi, S., Iyer, L.M., Kerzic, M.C., Aravind, L., Pancer, Z., Mariuzza, R.A. (2009). Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen. Nat Struct Mol Biol. 16(7):725-30.

2.      Iyer, L.M., Tahiliani, M., Rao, A., Aravind, L.  (2009). Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle. 27;8(11).

3.      Tahiliani, M., Koh, K.P., Shen, Y., Pastor, W.A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L.M., Liu, D.R., Aravind, L., Rao, A.(2009). Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science;324(5929):930-935.

4.      Venancio, T.M., Balaji, S., Iyer, L.M., Aravind L. (2009) Reconstructing the ubiquitin network - cross-talk with other systems and identification of novel functions. Genome Biology. 30;10(3):R33.

5.      Balaji, S., Iyer, L.M., Aravind, L. (2009). HPC2 and ubinuclein define a novel family of histone chaperones conserved throughout eukaryotes. Mol. BioSyst. Mol Biosyst.5(3):269-75.

6.      Burroughs, A.M., Iyer, L.M., Aravind, L. (2009). Natural history of the E1-like superfamily: Implication for adenylation, sulfur transfer, and ubiquitin conjugation. Proteins. Manuscript accepted for publication and available online from Oct 15 2008

7.      Iyer, L.M., Burroughs, A.M., Aravind, L. (2008). Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination. Biol Direct. 3;3:45.

8.      Iyer, L.M., Abhiman, S., Aravind, L. (2008). A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases. Biol Direct. 4;3:39.

9.      Balaji, S., Iyer L.M., Babu, M.M., Aravind, L. (2008). Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal? Trends Genet. 24(7):319-23.

10.  Iyer, L.M., Saraswathi A., Aravind, L. (2008) MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases. Biol Direct. 17;3:8.

11.  Saraswathi A., Iyer, L.M., Aravind, L. (2008) BEN: A novel domain in chromatin factors and DNA viral proteins. Bioinformatics. 24(4):458-461.

12.  Burroughs, A.M., Jaffee, M., Iyer, L.M., Aravind, L. (2008) Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation. J. Struc. Biol. 162(2):205-18.

13.  Iyer, L.M., Anantharaman, V., Wolf, M.Y., Aravind. L. (2008). Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes. Int J. Parasitol. 38(1):1-31.

14.  Lada, A.G., Iyer, L.M., Rogozin, I.B., Aravind, L., Pavlov, Yu.I. (2007). Incarnation of classical pro- and eukaryotic mechanisms of mutagenesis in hypermutagenesis and immunity of vertebrates. Russian Journal of Genetics. 3 (10): 1093-1107.

15.  Iyer, L.M. Anantharaman, V., Aravind, L. (2007). The DOMON domains are cytochromes and sugar sensors. Bioinformatics. 23(20):2660-2664.

16.  L. Aravind, Iyer, L.M., Wu, C. (2007). Domain architectures of the Scm3p protein provide insights into centromere function and evolution. Cell Cycle. 6(20):2511-2515.

17.  Burroughs A.M., Balaji S., Iyer L.M., Aravind L. (2007). Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold. Biol Direct. 2(1):18.

18.  Rogozin I.B., Iyer L.M.*, Liang L., Glazko G.V., Liston V.G., Pavlov Y.I., Aravind L., Pancer Z. (2007). Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase. Nat Immunol. 8(6):647-656.

19.  Anantharaman, V., Iyer, L.M., L. Aravind (2007). Comparative genomics of protists: new insights on evolution of eukaryotic signal transduction and gene regulation. Ann Rev. Micro. 61:453-475.

20.  Anantharaman, V., Iyer, L.M., Balaji, S., L. Aravind (2007). Adhesion molecules and other secreted host-interaction determinants in Apicomplexa: insights from comparative genomics. Int Rev Cytol. 262:1-74.

21.  Burroughs, A.M., Balaji, S., Iyer, L.M., Aravind, L. (2007). A novel superfamily containing the b-grasp fold involved in binding diverse soluble ligands. Biology Direct. 2:4.

22.  Burroughs, A.M., Iyer, L.M., Aravind, L. (2007). Comparative genomics and evolutionary trajectories of viral ATP dependent DNA-packaging systems. Genome dynamics. 3:48-65.

23.  Babu, M.M., Iyer, L.M.*, Balaji, S., Aravind, L. (2006). The natural history of the WRKY-GCM1 zinc fingers and the relationship between transcription factors and transposons. Nucleic Acids Research: 34(22):6505-20.

24.  Babu, M.M., Balaji, S., Iyer, L.M., Aravind, L. (2006). Estimating the prevalence and regulatory potential of the telomere looping effect in yeast transcription regulation. Cell Cycle: 5(20):2354-63.

25.  Iyer, L.M., Burroughs, A.M., Aravind, L. (2006) The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. Genome Biol.: 7(7):R60

26.  Balaji, S., Babu, M.M., Iyer, L.M., Luscombe, N.M., Aravind, L. (2006). Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. J. Mol. Biol.: 360(1):213-27.

27.  Balaji, S., Iyer, L.M., Aravind, L., Babu, M.M. (2006) Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks. J. Mol. Biol.: 360(1):204-12.

28.  Aravind, L., Iyer, L.M., Koonin, E.V. (2006). Comparative genomics and structural biology of the molecular innovations of eukaryotes. Curr Opin Struct Biol.: 16(3):409-19.

29.  Iyer, L.M., Babu, M.M., Aravind, L. (2006). The HIRAN domain and recruitment of chromatin remodeling and repair activities to damaged DNA. Cell Cycle: 5(7):775-82.

30.  Iyer, L.M., Balaji, S., Koonin, E.V., Aravind, L. (2006) Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res: 117(1):156-84.

31.  Iyer L.M., Burroughs A.M., Aravind L. (2006). The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism. Bioinformatics: 22(3):257-63.

32.  Wang T., Iyer L.M., Pancholy R., Shi X., Hall T.C. (2005). Assessment of penetrance and expressivity of RNAi-mediated silencing of the Arabidopsis phytoene desaturase gene. New Phytol. 167(3):751-60.

33.  Alder, M.N., Rogozin, I.B., Iyer, L.M., Glazko, G.V., Cooper, M.D., Pancer, Z. (2005). Diversity and function of adaptive immune receptors in a jawless vertebrate. Science: 310(5756):1970-3.

34.  Balaji S., Babu M.M., Iyer L.M., Aravind L. (2005). Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucleic Acids Res. 33(13):3994-4006

35.  Iyer L.M., Koonin E.V., Leipe D.D., Aravind L. (2005). Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members.. Nucleic Acids Res. 33(12):3875-3896

36.  L. Aravind, Anantharaman, V., Balaji, S., Babu, M.M., Iyer, L.M. (2005). The many faces of the helix-turn-helix domain: Transcription regulation and beyond. FEMS Micr. Rev. 2005 Apr;29(2):231-262.

37.  Tasneem, A., Iyer, L.M., Jakobsson, E. Aravind, L. (2005). Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels. Genome Biology. 2005;6(1):R4.

38.  Iyer, L.M., Koonin, E.V., Aravind, L. (2004). Novel predicted peptidases with a potential role in the ubiquitin signaling pathway. Cell Cycle. 6;3(11).

39.  Iyer, L.M., Makarova, K.S., Koonin, E.V., Aravind, L. (2004). Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division, and viral capsid packaging. Nuc. Acids. Res.32:5260-5279.

40.  Templeton, T.J., Iyer, L.M*, Anantharaman, V., Enomoto, S., Abrahante, J.E., Subramanian, G., Hoffman, S.L., Abrahamsen, M.S., Aravind, L. (2004). Comparative analysis of Apicomplexa and genomic diversity in eukaryotes. Genome Res. 14(9):1686-1695.

41.  Iyer, L.M., Aravind, L., Coon, S.L., Klein D.C., Koonin, E.V. (2004). Evolution of cell-cell signaling in animals:  Did late horizontal gene transfer from bacteria play a role? Trends Genet. 20(7):292-299.

42.  Iyer L.M., Koonin, E.V., Aravind, L. (2004). Evolution of the bacterial transcription system with respect to fine structure and lateral transfer of genes encoding polymerase subunits. Gene. 335:73-88.

43.  Pradel, G., Hayton, K., Aravind, L., Iyer,L.M., Abrahamsen, M.S., Bonawitz, A., Templeton, T.J. (2004) An Apicomplexan LCCL Domain-Containing Protein Family Expressed During Plasmodium falciparum Mosquito Transmission. J. Exp. Med. 199(11):1533-1544.

44.  Abrahamsen, M.S., Templeton, T.J., Enomoto, S., Abrahante, J.E., Zhu, G., Lancto, C.A., Deng, M., Liu, C., Widmer, G., Tzipori, S., Buck, G.A., Xu, P., Bankier, A.T., Dear, P.H., Konfortov, B.A., Spriggs, H.F., Iyer, L., Anantharaman, V., Aravind, L., Kapur V. (2004). Complete genome sequence of the apicomplexan, Cryptosporidium parvum Science. 304(5669):441-445.

45.  Aravind, L., Iyer, L.M., Leipe, D.D., Koonin, E.V. (2004) A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain. Genome Biology. 5(5):R30.

46.  Iyer, L.M., Aravind, L. (2004). The emergence of catalytic and structural diversity within the beta clip fold. Proteins. 55(4):977-991.

47.  Iyer, L.M., Leipe, D.D., Koonin, E.V. Aravind, L. (2004).  Evolutionary history and higher order classification of AAA+ ATPases. J Str. Biol. 146(1-2):11-31.

48.  Aravind, L., Iyer, L.M., Wellems, T.E., Miller, L.H. (2003). Plasmodium Biology: Genomic Gleanings. Cell. 115: 771-785.

49.  Aravind, L., Anantharaman, V., Iyer, L.M. (2003). Evolutionary connections between bacterial and eukaryotic signaling systems: a genomic perspective. Curr. Op. Micro. 6(5):490-497.

50.  Aravind, L., Iyer, L.M., Anantharaman, V. (2003). The two faces of Alba: the evolutionary connection between proteins functioning in chromatin structure and RNA metabolism. Genome Biology.  4:R64.

51.  Aravind, L., Iyer, L.M. (2003). Provenance of SET-domain histone methyltransferases through duplication of a simple structural unit. Cell Cycle: 2(4):369-376.

52.  Aravind, L., Iyer, L.M., and Koonin, E.V. (2003).  Scores of  RINGs but no PHDs in ubiquitin signaling. Cell Cycle: 2(2): 123-126.

53.  Iyer, L.M., Koonin, E.V., and Aravind, L. (2003). Evolutionary connection between the catalytic subunits of the DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA polymerases and the origin of RNA polymerases. BMC Struc. Biol:  3(1):1.

54.  Iyer, L.M., Anantharaman, V. and Aravind, L. (2003). Ancient conserved domains shared by animal soluble guanylyl cyclases and bacterial signaling proteins. BMC Genomics: 4:5.

55.  Mazumder, R., Iyer, L.M*,  Vasudevan S., Aravind,  L. (2002). Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily. Nuc. Acids. Res. 30(23):5229-5243.

56.  Iyer, L.M. and Aravind, L. (2002). The catalytic domains of thiamine triphosphatase and CyaB-like adenylyl cyclases define a novel superfamily of domains that bind organic phosphates. BMC Genomics.  3(1): 33.

57.  Aravind, L. and Iyer, L.M. (2002). Intra-proteomic networks: New forays into predicting interaction-partners. Genome Res. 12: 1156-1158.

58.  Aravind, L., and Iyer, L.M. (2002).  The SWIRM domain: A conserved module found in chromosomal proteins points to novel chromatin modifying activities. Genome Biol. 3(8): 0039.1-0039.7.

59.  Iyer, L.M., Koonin, E.V., and Aravind, L. (2002). Classification and evolutionary history of the single strand annealing proteins, RecT,  Redb, ERF and RAD52. BMC Evol. Biol. 3(1):8.

60.  Iyer, L.M., Koonin, E.V., and Aravind L. (2002). Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors.  Genome Biol. 3(3): 0012.1-0012.11.

61.  Iyer, L.M.,  Aravind. L, Bork, P., Hofmann, K., Mushegian, A.R., Zhulin, I.B.,  and Koonin, E.V. (2001). Quod erat demonstrandum? The mystery of experimental validation of erroneous computational analyses of protein sequences. Genome Biol. 2(12): 0051.1-0051.11. 

62.  Iyer, L.M., Aravind, L.,  and Koonin, E.V. (2001). A common origin of four diverse families of large eukaryotic DNA viruses. J. Virol. 75(23): 11720-11734.

63.  Iyer, L.M., Koonin, E.V., and Aravind, L (2001). Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily. Proteins. 43(2):134-44.

64.  Hall, T.C., Kumpatla, S.P., Kharb, P., Iyer, L., Cervera, M., Jiang, Y., Wang, T., Xang, G., Teerawanichpan, P., Narangajavana,  and J., Dong, J. (2001) Gene silencing and its reactivation in transgenic rice, Rice Genetics IV, Science Publishers Inc., New Delhi (India)and International Rice Research Institute, Los Banos (Philippines): 465-481.

65.  Iyer, L.M., Kumpatla, S.P., Chandrasekharan, M.B. and Hall, T.C. (2000). Transgene silencing in monocots. Plant Mol. Biol. 43 (2/3), 323-346.

66.  Iyer, L.M. and Hall, T.C. (2000). Virus recovery is induced in Brome mosaic virus p2 transgenic plants showing synchronous complementation and RNA‑2 specific silencing. Mol. Plant‑Microbe Interact.13 (3), 247-258.

67.  Kumpatla, S. P., Chandrasekharan, M. B., Iyer, L.M., Li, G., and Hall, T. C. (1998). Genome intruder scanning and modulation systems and transgene silencing. Trends in Plant Science 3(3), 97-104.

68.  Shivapriya, R., Prasad, R., Narayanan, I. L., Krishnaswamy, S., and Dharmalingam, K. (1995). Expression of the mcrA gene of Escherichia coli is regulated posttranscriptionally, possibly by sequestration of the Shine-Dalgarno region. Gene 157(1-2), 201-7.

 

Note: * joint first-author

 

Book Chapters

1.      Iyer, L.M., Aravind, L. (2006). Phyletic Distribution And Evolutionary Relatedness Of Proteins Involved In Prereplication Complex Assembly.  In DNA Replication and Human Disease Cold Spring Harbor Laboratory Press, Cold Spring Harbor , NY.

 

Oral and Poster Presentations

 

  1. Iyer, L.M.,  Anantharaman, V., Balaji, S., Aravind, L. Uncovering specific transcription factors in parasitic protists and understanding their evolutionary histories. 19th Annual Molecular Parasitology Meeting.. Woodshole, MA. Sept.  21-25, 2008
  2. Iyer, L.M. Comparative genomics of apicomplexan surface and secreted proteins involved in host-pathogen interactions. CBB Seminar, NIH, Oct 23, 2007.
  3. Iyer, L,M. The origins of the ubiqutin signaling pathway. CBB Seminar, NIH, May 01, 2007.
  4. Iyer, L,M., Burroughs, A.M., Balaji, S., Aravind, L. An Evolutionary perspective on the functional and structural diversity of the ubiquitin superfamily. Cold Spring Harbor Laboratory Meeting. April 25-29, 2007.
  5. Burroughs, A.M., Iyer, L,M., Aravind, L. Genomic analysis uncovers novel prokaryotic ubiquitin-signaling systems. Cold Spring Harbor Laboratory Meeting. April 25-29, 2007.
  6. Natarajan, S., Asba, T., Varma, S., Iyer, L., Aravind, L., Jakobsson, E. Towards a physics and systems understanding of ion transport in prokaryotes. DOE Genomics-GTL Contractor-Grantee Workshop III. Washington D.C., Feb 6-9, 2005.
  7. Tasneem, A., Iyer, L.M., Jakobsson, E. and Aravind, L.  Identification of the prokaryotic ligand-gated ion channels and their implications for the origins and mechanisms of animal Cys-loop ion channels. 15th Annual Frederick Conference on CE/Proteomics. Oct 18-19, 2004.
  8. Iyer, L,M. Evolution of cell-cell signaling in animals: did late horizontal gene transfer from bacteria have a role? Laboratory of Developmental Neurobiology, NICHD seminar, NIH, Feb 6 2004.
  9. Iyer, L,M. Lessons on virus evolution from comparative genomics of Nucleo-cytoplasmic large DNA viruses. CBB Seminar, NIH, Dec 20, 2005.
  10. Iyer, L,M. Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division, and viral capsid packaging, CBB Seminar, NIH, Sept. 28, 2004.
  11. Iyer, L.M. The Evolutionary histories of the DNA dependent RNA polymerase and eukaryotic RNA dependent RNA polymerase and the multidomain nature of the DNA dependent RNA polymerase. CBB Seminar, NIH. Mar, 04, 2003.
  12. Iyer, L.M. and Hall, T.C. Systemic infection studies of Brome mosaic virus in p2 transgenic plants. American Society for Virology 18th Annual Meeting, Amherst, MA. Jul 10-14, 1999.
  13. Templeton, T.J., Aravind, L. Enomoto, S., Abrahante Llorens J.E., Iyer, L., Anantharaman, V., Kapur, V., Abrahamsen M.S. Molecular Parasitology Meeting XIV. Sept. 14-18, 2003.
  14. Hall, T.C. and Iyer, L. Gene-specific silencing of BMV RNA. 7th International Congress of Plant Pathology, Edinburgh, Scotland.  Aug 9-16, 1998.
  15. Iyer, L. and Hall, T. C. Gene-specific silencing of Brome mosaic virus RNA.  American Society for Virology 17th Annual Meeting. Vancouver, BC, Canada.  July 11-15, 1998.
  16. Iyer, L. and Hall, T. C. Homology- based silencing in the BMV genome. American Society for Virology 15th Annual Meeting. Ontario, Canada. Jul 13-17, 1996.
  17. Iyer, L. and Hall, T. C.  Homology-based silencing in the BMV genome.  Noble Foundation Virology Group Meeting.  Ardmore, OK.  Jan 12-14, 1996.
  18. Hall, T.C., Duggal, R., and Iyer, L.M.  Evidence for the participation of host proteins in (+)strand synthesis during replication of Brome mosaic virus RNA.  IVth international positive strand RNA virus symposium.  Utrecht, the Netherlands, May 1995.
  19. Iyer, L.M., Duggal, R. and Hall, T. C.  Effect on BMV RNA replication of small BMV RNA fragments containing ICR motifs.  American Society for Virology 14th Annual Meeting.  Austin, Texas.  Jul 8-12, 1995.

 

Referee experience

 

BMC Genomics, BMC Evolutionary Biology, Biochimica et Biophysica Acta, Bioinformatics, Developmental Cell, Gene, Journal of Molecular Biology, Molecular Genetics and Genomics, Nature Biotechnology, Nucleic Acids Research, PLOS Biology, Trends in Biochemical Sciences, Trends in Immunology, Minority Access to Research Careers fellowship grant.

 

Editorial board

Biology Direct, Discovery Notes section.

 

Teaching experience

 

1993-94, 1996-97, Fall 1999. Graduate Teaching assistant. Department of biology. Taught laboratory courses in Immunology, Medical Microbiology and General Microbiology to undergraduate students ranging from juniors to seniors.

 

Professional Societies

 

Sigma Xi 2005-,

American Society for Virology, 1998, 1999.