Identification and characterization of functional homologs of nitrogenase cofactor biosynthesis protein NifB from methanogens

Nitrogenase biosynthesis protein NifB catalyzes the radical S-adenosyl-L-methionine (SAM)-dependent insertion of carbide into the M cluster, the cofactor of the molybdenum nitrogenase from Azotobacter vinelandii. Here, we report the identification and characterization of two naturally “truncated” homologs of NifB from Methanosarcina acetivorans (NifBMa) and Methanobacterium thermoautotrophicum (NifBMt), which contain a SAM-binding domain at the N terminus but lack a domain toward the C terminus that shares homology with NifX, an accessory protein in M cluster biosynthesis. NifBMa and NifBMt are monomeric proteins containing a SAM-binding [Fe4S4] cluster (designated the SAM cluster) and a [Fe4S4]-like cluster pair (designated the K cluster) that can be processed into an [Fe8S9] precursor to the M cluster (designated the L cluster). Further, the K clusters in NifBMa and NifBMt can be converted to L clusters upon addition of SAM, which corresponds to their ability to heterologously donate L clusters to the biosynthetic machinery of A. vinelandii for further maturation into the M clusters. Perhaps even more excitingly, NifBMa and NifBMt can catalyze the removal of methyl group from SAM and the abstraction of hydrogen from this methyl group by 5′-deoxyadenosyl radical that initiates the radical-based incorporation of methyl-derived carbide into the M cluster. The successful identification of NifBMa and NifBMt as functional homologs of NifB not only enabled classification of a new subset of radical SAM methyltransferases that specialize in complex metallocluster assembly, but also provided a new tool for further characterization of the distinctive, NifB-catalyzed methyl transfer and conversion to an iron-bound carbide.

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Genome-Wide Identification and Characterization of CIPK Family and Analysis Responses to Various Stresses in Apple (Malus domestica)

International Journal of Molecular Sciences ◽

10.3390/ijms19072131 ◽

2018 ◽

Vol 19 (7) ◽

pp. 2131 ◽

Cited By ~ 8

Author(s):

Lili Niu ◽

Biying Dong ◽

Zhihua Song ◽

Dong Meng ◽

Yujie Fu

Keyword(s):

Growth Stages ◽

Hormone Signaling ◽

Chromosomal Distribution ◽

Interacting Protein ◽

C Terminus ◽

Genome Wide ◽

Enhanced Expression ◽

Interaction Domains ◽

Identification And Characterization

In the CIPK family, the CBL-interacting protein kinases have shown crucial roles in hormone signaling transduction, and response to abiotic stress in plant developmental processes. The CIPK family is characterized by conserved NAF/FISL (Asn-Ala-Phe) and PPI (protein-phosphatase interaction) domains in the C-terminus. However, little data has been reported about the CIPK family in apple. A total of 34 MdCIPK genes were identified from the apple genome in this study and were later divided into two groups according to the CIPK domains, characterized by gene structure and chromosomal distribution, and then mapped onto 17 chromosomes. All MdCIPK genes were expressed in the four apple tissues (leaf, root, flower, and fruit). In addition, the MdCIPK gene expression profile showed that five members among them revealed enhanced expression during the pollen tube growth stages. The MdCIPK4 was the most expressive during the entire fruit development stages. Under stress conditions 21 MdCIPK genes transcript levels were up-regulated in response to fungal and salt treatments. This suggested the possible features of these genes’ response to stresses in apples. Our findings provide a new insight about the roles of CIPK genes in apples, which could contribute to the cloning and functional analysis of CIPK genes in the future.

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Identification and characterization of the rice pre‐harvest sprouting mutants involved in molybdenum cofactor biosynthesis

New Phytologist ◽

10.1111/nph.15607 ◽

2018 ◽

Vol 222 (1) ◽

pp. 275-285 ◽

Cited By ~ 1

Author(s):

Xin Liu ◽

Jing Wang ◽

Yang Yu ◽

Lina Kong ◽

Yimei Liu ◽

...

Keyword(s):

Molybdenum Cofactor ◽

Cofactor Biosynthesis ◽

Molybdenum Cofactor Biosynthesis ◽

Identification And Characterization

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Coordinated Action of NRPS, Baeyer-Villiger Monooxygenase, and Methyltransferase Ensures the Economical Biosynthesis of Bohemamines in Streptomyces sp. CB02009

10.26434/chemrxiv.11687139 ◽

2020 ◽

Author(s):

Ling Liu ◽

Sainan Li ◽

Runze Sun ◽

Xiangjing Qin ◽

Jianhua Ju ◽

...

Keyword(s):

Methyl Groups ◽

Ribosome Engineering ◽

Methyl Group ◽

Proteinogenic Amino Acid ◽

Streptomyces Sp ◽

Coordinated Action ◽

Peptide Synthetase ◽

Identification And Characterization ◽

Shed Light

Bohemamines (BHMs) are bacterial alkaloids containing a pyrrolizidine core with two unprecedented methyl groups. Herein we report the activation of BHMs biosynthesis in Streptomyces sp. CB02009 using a ribosome engineering approach. Identification and characterization of the bhm gene cluster reveals a coordinated action of nonribosomal peptide synthetase BhmJ, Baeyer-villiger monooxygenase BhmK and methyltransferase BhmG for BHMs biosynthesis. BhmG is responsible for the C-methylation on C-7, while the C-9 methyl group is from a non-proteinogenic amino acid (2S,5S)-5-methylproline, required for BHMs production in three model Streptomyces hosts. Our study shed light on the intricate interaction of BhmJ/BhmK/BhmG for the economical biosynthesis of BHMs in their native producer, and also unraveled that BhmJ and BhmK are competent biocatalysts in Streptomyce albus.

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Identification and Characterization of two nitrogen fixation regulatory regions, nifA and nfrX, in Azotobacter vinelandii and Azotobacter chroococcum

Molecular Microbiology ◽

10.1111/j.1365-2958.1988.tb00033.x ◽

1988 ◽

Vol 2 (3) ◽

pp. 303-314 ◽

Cited By ~ 34

Author(s):

E. Santero ◽

A. Toukdarian ◽

R. Humphrey ◽

C. Kennedy

Keyword(s):

Nitrogen Fixation ◽

Azotobacter Vinelandii ◽

Azotobacter Chroococcum ◽

Regulatory Regions ◽

Identification And Characterization

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Identification and characterization of a novel calmodulin binding site in Drosophila TRP C-terminus

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2018.05.007 ◽

2018 ◽

Vol 501 (2) ◽

pp. 434-439 ◽

Cited By ~ 3

Author(s):

ZiLing Sun ◽

YunHua Zheng ◽

Wei Liu

Keyword(s):

Binding Site ◽

Calmodulin Binding ◽

C Terminus ◽

Identification And Characterization

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Identification and characterization of a new human ETS-family transcription factor, TEL2, that is expressed in hematopoietic tissues and can associate with TEL1/ETV6

Blood ◽

10.1182/blood.v95.11.3341.011k44_3341_3348 ◽

2000 ◽

Vol 95 (11) ◽

pp. 3341-3348 ◽

Cited By ~ 5

Author(s):

Mark D. Potter ◽

Arjan Buijs ◽

Brent Kreider ◽

Luc van Rompaey ◽

Gerard C. Grosveld

Keyword(s):

Dna Binding ◽

Regulatory Protein ◽

Binding Assays ◽

Core Motif ◽

Ets Proteins ◽

C Terminus ◽

Ets Family ◽

Binding Sequence ◽

Identification And Characterization

The ETS family of proteins is a large group of transcription factors implicated in many aspects of normal hematopoietic development, as well as oncogenesis. For example, the TEL1/ETV6 (TEL1) gene is required for normal yolk sac angiogenesis, adult bone marrow hematopoiesis, and is rearranged or deleted in numerous leukemias. This report describes the cloning and characterization of a novelETS gene that is highly related to TEL1 and is therefore called TEL2. The TEL2 gene consists of 8 exons spanning approximately 21 kilobases (kb) in human chromosome 6p21. Unlike the ubiquitously expressed TEL1 gene, however,TEL2 appears to be expressed predominantly in hematopoietic tissues. Antibodies raised against the C-terminus of the TEL2 protein were used to show that TEL2 localizes to the nucleus. All ETS proteins can bind DNA via the highly conserved ETS domain, which recognizes a purine-rich DNA sequence with a GGAA core motif. DNA binding assays show that TEL2 can bind the same consensus DNA binding sequence recognized by TEL1/ETV6. Additionally, the TEL2 protein is capable of associating with itself and with TEL1 in doubly transfected Hela cells, and this interaction is mediated through the pointed (PNT) domain of TEL1. The striking similarities ofTEL2 to the oncogenic TEL1, its expression in hematopoietic tissues, and its ability to associate withTEL1 suggest that TEL2 may be an important hematopoietic regulatory protein.

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Identification and characterization of a new human ETS-family transcription factor, TEL2, that is expressed in hematopoietic tissues and can associate with TEL1/ETV6

Blood ◽

10.1182/blood.v95.11.3341 ◽

2000 ◽

Vol 95 (11) ◽

pp. 3341-3348 ◽

Cited By ~ 41

Author(s):

Mark D. Potter ◽

Arjan Buijs ◽

Brent Kreider ◽

Luc van Rompaey ◽

Gerard C. Grosveld

Keyword(s):

Dna Binding ◽

Regulatory Protein ◽

Binding Assays ◽

Core Motif ◽

Ets Proteins ◽

C Terminus ◽

Ets Family ◽

Binding Sequence ◽

Identification And Characterization

Abstract The ETS family of proteins is a large group of transcription factors implicated in many aspects of normal hematopoietic development, as well as oncogenesis. For example, the TEL1/ETV6 (TEL1) gene is required for normal yolk sac angiogenesis, adult bone marrow hematopoiesis, and is rearranged or deleted in numerous leukemias. This report describes the cloning and characterization of a novelETS gene that is highly related to TEL1 and is therefore called TEL2. The TEL2 gene consists of 8 exons spanning approximately 21 kilobases (kb) in human chromosome 6p21. Unlike the ubiquitously expressed TEL1 gene, however,TEL2 appears to be expressed predominantly in hematopoietic tissues. Antibodies raised against the C-terminus of the TEL2 protein were used to show that TEL2 localizes to the nucleus. All ETS proteins can bind DNA via the highly conserved ETS domain, which recognizes a purine-rich DNA sequence with a GGAA core motif. DNA binding assays show that TEL2 can bind the same consensus DNA binding sequence recognized by TEL1/ETV6. Additionally, the TEL2 protein is capable of associating with itself and with TEL1 in doubly transfected Hela cells, and this interaction is mediated through the pointed (PNT) domain of TEL1. The striking similarities ofTEL2 to the oncogenic TEL1, its expression in hematopoietic tissues, and its ability to associate withTEL1 suggest that TEL2 may be an important hematopoietic regulatory protein.

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Identification and Characterization of Banana Bract Mosaic Virus in India

Plant Disease ◽

10.1094/pdis.1997.81.6.669 ◽

1997 ◽

Vol 81 (6) ◽

pp. 669-672 ◽

Cited By ~ 30

Author(s):

B. C. Rodoni ◽

Y. S. Ahlawat ◽

A. Varma ◽

J. L. Dale ◽

R. M. Harding

Keyword(s):

Particle Morphology ◽

Nucleic Acid Hybridization ◽

Mosaic Symptom ◽

Sequence Comparisons ◽

Protein Coding ◽

C Terminus ◽

Amino Acid Levels ◽

Cucumber Mosaic Cucumovirus ◽

Identification And Characterization

We have identified banana bract mosaic potyvirus (BBMV) in banana plants growing in the Coimbatore and Tiruchchirappalli regions of southern India based on symptomatology, particle morphology, sequence homology, and nucleic acid hybridization assays. Potyvirus-like particles typical of BBMV also were detected in sap dips from banana plants growing in Maharashtra State. Sequence comparisons of the C terminus of the coat protein-coding and 3′ untranslated regions revealed that the Indian isolates of BBMV had greater than 96.6 and 97.2% homology with a Philippines isolate at the nucleotide and amino acid levels, respectively. BBMV-infected banana cultivars from the Coimbatore region showed the characteristic mosaic on the bract of the banana inflorescence. In contrast, infected plants growing in the Tiruchchirappalli region and Maharashtra State displayed symptoms similar to those associated with cucumber mosaic cucumovirus and not the characteristic bract mosaic symptom. These results indicate that BBMV is more widespread than previously thought.

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Identification and Characterization of the Most Abundant Cellulases in Stylet Secretions from Globodera rostochiensis

Phytopathology ◽

10.1094/phyto-99-2-0194 ◽

2009 ◽

Vol 99 (2) ◽

pp. 194-202 ◽

Cited By ~ 30

Author(s):

Sajid Rehman ◽

Patrick Butterbach ◽

Herman Popeijus ◽

Hein Overmars ◽

Eric L. Davis ◽

...

Keyword(s):

Expressed Sequence Tag ◽

Specific Activity ◽

Glycosyl Hydrolase ◽

Globodera Rostochiensis ◽

Cyst Nematodes ◽

C Terminus ◽

Different Types ◽

Identification And Characterization ◽

Expressed Sequence

Plant-parasitic cyst nematodes secrete cell wall modifying proteins during their invasion of host plants. In this study, we used a monoclonal antibody to immunopurify and to sequence the N terminus of the most abundant cellulases in stylet secretions of preparasitic juveniles of Globodera rostochiensis. The N-terminal amino acid sequence perfectly matched the sequence of an expressed sequence tag of two nearly identical genes, named Gr-eng3 and Gr-eng4, which show relatively low similarity with the previously identified Gr-eng1 and Gr-eng2 (i.e., 62% similarity and 42% identity). The recombinantly produced proteins from Gr-eng3 and Gr-eng4 demonstrated specific activity on carboxymethylcellulose, indicating that these genes encode active cellulases. To date, the cellulases in cyst nematodes are comprised of three possible domain structure variants with different types of ancillary domains at the C terminus of the glycosyl hydrolase family 5 (GHF5) domain. We used Bayesian inference to show that the phylogeny of the GHF5 domain based on currently available data suggest that the extant nematode cellulases arose through reshuffling of the GHF5 domain with different types of ancillary domains as relatively independent units. Knocking-down Gr-eng3 and Gr-eng4 using RNA interference resulted in a reduction of nematode infectivity by 57%. Our observations show that the reduced infectivity of the nematodes can be attributed to poor penetration of the host's root system at the onset of parasitism.

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