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Evolutionary and Functional Relationships in the Truncated Hemoglobin Family

Juan P. Bustamante, Leandro Radusky, Leonardo Boechi, Darío A. Estrin, Arjen ten Have, Marcelo A. Martí, Ozlem Keskin
2016 PLoS Computational Biology  
Evolutionary and Functional Relationships in Globins PLOS Computational Biology |  ...  The truncated hemoglobin family presents an interesting benchmark study due to their ubiquity, sequence diversity in the context of a conserved fold and the number of characterized members.  ...  Evolutionary and Functional Relationships in Globins environment.  ... 
doi:10.1371/journal.pcbi.1004701 pmid:26788940 pmcid:PMC4720485 fatcat:r7iesqio5zf5roxr3fqojw422m

Plant hemoglobins: Important players at the crossroads between oxygen and nitric oxide

Kapuganti J. Gupta, Kim H. Hebelstrup, Luis A.J. Mur, Abir U. Igamberdiev
2011 FEBS Letters  
This evolutionary tendency is observed in the family of Cannabaceae in two genera, Trema and Parasponia [36, 37] .  ...  We will now further elaborate on the structure-functional and evolutionary basis of the plant hemoglobin classes.  ... 
doi:10.1016/j.febslet.2011.10.036 pmid:22036787 fatcat:w3dcqlhgerfm3cvotdt7vssvy4

Structure and chromosomal arrangement of leghemoglobin genes in kidney bean suggest divergence in soybean leghemoglobin gene loci following tetraploidization

J S Lee, D P Verma
1984 EMBO Journal  
A large deletion in one of the two four-gene loci in soybean resulted in the generation of the Lbc(2) locus containing two leghemoglobin genes, one functional and another pseudo (LbPsi(2)).  ...  The two other truncated genes (LbT(1) and LbT(2)) were probably generated similarly in the genome of Glycine spp. following tetraploidization before the divergence of G. max and G. soja.  ...  J.Slightom and M.Murray for providing the Phaseolus genomic library, and Drs. G.Brown and E.Olson for their critical comments on this manuscript. The secretarial assistance of Miss Y.  ... 
pmid:16453577 pmcid:PMC557762 fatcat:i2fijkqckbfvzpcrmok45pp7uq

Evolutionary trace analysis of plant haemoglobins: implications for site-directed mutagenesis

Duvvuru muni Rajasekhara Reddy
2007 Bioinformation  
Results indicate that the, evolutionary trace method like conventional phylogentic analysis, could resolve phylogentic relationships between plant haemoglobin family.  ...  To determine functionally important residues in non-symbiotic haemoglobins, I have analyzed a number of sequences from plant haemoglobin family, in the context of the known crystal structures of plant  ...  that are members of the 'truncated hemoglobin' family.  ... 
doi:10.6026/97320630001370 pmid:17597924 pmcid:PMC1891720 fatcat:lev37a5y7nebfltfntifmiv3su

New-old hemoglobin-like proteins of symbiotic dinoflagellates

Nedeljka N. Rosic, William Leggat, Paulina Kaniewska, Sophie Dove, Ove Hoegh-Guldberg
2013 Ecology and Evolution  
Furthermore, the inducible nature of Hb-2 gene by both thermal and nutrient stressors indicates a prospective role of this form of hemoglobin in the initial coral-algal responses to changes in environmental  ...  (type C3), we discovered the sequences of two novel and highly polymorphic hemoglobin-like genes and proposed their 3D protein structures.  ...  ) to OHG and SD.  ... 
doi:10.1002/ece3.498 pmid:23610627 pmcid:PMC3631397 fatcat:o7cp34oogzfszi7wottdviwhly

Novel Hemoglobin from Synechocystis sp. PCC 6803: Shedding Light on the Structure-Function Relationship and Its Biotechnological Applications [chapter]

Mohd. Asim Khan, Sheetal Uppal, Suman Kundu
2021 Cyanobacteria - Recent Advances in Taxonomy and Applications [Working Title]  
Since then, the newly identified globins in the cyanobacteria are raising intriguing questions about their structure and physiological functions, which are quite different from vertebrate's hemoglobin  ...  PCC 6803, its interacting protein partners, proposed functions, and its biotechnological implications including potential in the field of artificial oxygen carriers.  ...  These classes of hemoglobins are called "truncated hemoglobins (TrHbs)" and constitute a major class of the globin family [14] .  ... 
doi:10.5772/intechopen.97699 fatcat:uirpo2jyifdzzo5v2ni4m3shhi

Spectral distortion measures for biological sequence comparisons and database searching

Tuan D. Pham
2007 Pattern Recognition  
of relationships between genes, proteins and species; and the discovery of novel protein structures and functions.  ...  In bioinformatics and computational biology, methods for biological sequence comparison play the most important role for the interpretation of complex nucleotide and protein data such as the inference  ...  Acknowledgements The author acknowledges the assistance of Byung-Sub Shim who provided the information on the protein sequences and carried out the computer implementation of the proposed methods under  ... 
doi:10.1016/j.patcog.2006.02.026 fatcat:ixuzvq3adne3pcosxjh2x6bwwu

The Genomic Record of Humankind's Evolutionary Roots

Morris Goodman
1999 American Journal of Human Genetics  
The assistance of Elaine Krobock and Scott L. Page in formatting the Appendix and figure 1 is much appreciated.  ...  Acknowledgments This work has been supported by grants from the National Science Foundation (INT-9602913) and the National Institutes of Health (HL33940).  ...  The emergence in anthropoid primates of a fetal hemoglobin that unloads oxygen in tissues more readily than does adult hemoglobin correlates with the evolutionary trend that prolonged fetal life.  ... 
doi:10.1086/302218 pmid:9915940 pmcid:PMC1377699 fatcat:iupidzrwu5f47dmryklc2k2d5e

The truncated hemoglobins in the Antarctic psychrophilic bacterium Pseudoalteromonas haloplanktis TAC125

Daniela Giordano, Ermenegilda Parrilli, Agnes Dettaï, Roberta Russo, Giulia Barbiero, Gennaro Marino, Guillaume Lecointre, Guido di Prisco, Luisa Tutino, Cinzia Verde
2007 Gene  
Identifying the bases of protein adaptation to higher or lower temperatures is important to understand the relationship between structure/function and life history on the Earth.  ...  The P. haloplanktis TAC125 genome contains three genes in distinct positions on chromosome I, named PSHAa0030, PSHAa2217 and PSHAa0458. These genes encode three truncated hemoglobins.  ...  Acknowledgements We thank Angela Amoresano and Giovanni Chiappetta for the molecular mass measurements by mass spectrometry, and Vito Carratore for the skillful technical assistance in amino-acid sequencing  ... 
doi:10.1016/j.gene.2007.02.037 pmid:17582708 fatcat:xs6l7utoarffzinu3erohe2l5q

Transcriptomes reveal expression of hemoglobins throughout insects and other Hexapoda

Hollister W. Herhold, Steven R. Davis, David A. Grimaldi, Marc Robinson-Rechavi
2020 PLoS ONE  
Discovery and identification of 1333 putative hemoglobins were achieved with target-gene BLAST searches of the NCBI TSA database, verifying functional residues, secondary- and tertiary-structure predictions  ...  Their derivation and co-option from early neuroglobins may explain the widespread nature of hemoglobins in various kingdoms and phyla.  ...  Acknowledgments Special thanks to Apurva Narechania and Sajesh Singh for their assistance with running our analyses on the AMNH high-performance computing clusters.  ... 
doi:10.1371/journal.pone.0234272 pmid:32502196 fatcat:aa26tif7t5bxppi355q2jk2w3q

Gene Turnover in the Avian Globin Gene Families and Evolutionary Changes in Hemoglobin Isoform Expression

Juan C. Opazo, Federico G. Hoffmann, Chandrasekhar Natarajan, Christopher C. Witt, Michael Berenbrink, Jay F. Storz
2014 Molecular biology and evolution  
To investigate this possibility and to explore the phenotypic consequences of variation in gene copy number, we examined evolutionary changes in the families of genes that encode the aand b-type subunits  ...  The apparent stasis in the evolution of avian chromosomes suggests that birds may have experienced relatively low rates of gene gain and loss in multigene families.  ...  Acknowledgments The authors thank T. Valqui, E. Bautista, and the students and staff of the MSB Bird Division and CORBIDI for assistance with field collections. The authors also thank E. D.  ... 
doi:10.1093/molbev/msu341 pmid:25502940 pmcid:PMC4379397 fatcat:7yug3qs53rcxfdgcl4swjqj3nq

Rapid comparison of properties on protein surface

Lee Sael, David La, Bin Li, Raif Rustamov, Daisuke Kihara
2008 Proteins: Structure, Function, and Bioinformatics  
ACKNOWLEDGMENTS The authors thank Vishwesh Venkatraman for invaluable assistance in the preparation of this paper.  ...  (B) four globin proteins of diverged evolutionary distance, leghemoglobin from Lupinus luteus (1gdi), human brain neuroglobin (1oj6A), myoglobin from yellowfin tuna (1myt), and group II truncated hemoglobin  ...  The four globins shown here are all monomeric, but have a distant evolutionary relationship (i.e., the sequence identity between them is low), a varied range of affinity to oxygen, and different functions  ... 
doi:10.1002/prot.22141 pmid:18618695 pmcid:PMC2574582 fatcat:lzdr7xxa3ze7ng2jqhmg4fld4m

Globin-coupled sensors, protoglobins, and the last universal common ancestor

T FREITAS, J SAITO, S HOU, M ALAM
2005 Journal of Inorganic Biochemistry  
Functional and evolutionary analyses of the GCSs, their protoglobin ancestor, and their relationship to the last universal common ancestor (LUCA) are discussed in the context of globin-based signal transduction  ...  Globincoupled sensors (GCSs) were first described as regulators of the aerotactic responses in Bacillus subtilis and Halobacterium salinarum.  ...  Acknowledgement This investigation was supported by a National Science Foundation Grant MCB0080125 and by a University of Hawaii intramural grant (M.A.).  ... 
doi:10.1016/j.jinorgbio.2004.10.024 pmid:15598488 fatcat:qik2kbeshnh7fnptpdmouisoai

BacHbpred: Support Vector Machine Methods for the Prediction of Bacterial Hemoglobin-Like Proteins

MuthuKrishnan Selvaraj, Munish Puri, Kanak L. Dikshit, Christophe Lefevre
2016 Advances in Bioinformatics  
The recent upsurge in microbial genome data has revealed that hemoglobin-like (HbL) proteins may be widely distributed among bacteria and that some organisms may carry more than one HbL encoding gene.  ...  We also compared the performance of our proposed models in homology detection databases. The performance of the different approaches was estimated using fivefold cross-validation techniques.  ...  The authors also thank the Department of Biotechnology, Punjabi University; IMTECH, India; and Deakin University, Australia, for supporting collaborative research.  ... 
doi:10.1155/2016/8150784 pmid:27034664 pmcid:PMC4789356 fatcat:kfixjacctbdmpnkhz4cwkk7n6a

An evolutionary treasure: unification of a broad set of amidohydrolases related to urease

Liisa Holm, Chris Sander
1997 Proteins: Structure, Function, and Bioinformatics  
Two member families are common to archaea, eubacteria, and eukaryota.  ...  Thirteen other functions supported by the same structural motif and conserved chemical mechanism apparently represent later adaptations for different substrate specificities in different cellular contexts  ...  does not cleave hemoglobin 34 ; and repeated recruitments of enzymes as structural proteins in the eye lens. 35 There is some information about the function of the noncatalytic members of the superfamily  ... 
doi:10.1002/(sici)1097-0134(199705)28:1<72::aid-prot7>3.3.co;2-t pmid:9144792 fatcat:nxquno2okzbs7isab5k7pq5qkq
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