Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase

Abstract

Members of the DUF34 (domain of unknown function 34) family, also known as the NIF3 protein superfamily, are ubiquitous across superkingdoms. Proteins of this family have been widely annotated as “GTP cyclohydrolase I type 2” through electronic propagation based on one study. Here, the annotation status of this protein family was examined through a comprehensive literature review and integrative bioinformatic analyses that revealed varied pleiotropic associations and phenotypes. This analysis combined with functional complementation studies strongly challenges the current annotation and suggests that DUF34 family members may serve as metal ion insertases, chaperones, or metallocofactor maturases. This general molecular function could explain how DUF34 subgroups participate in highly diversified pathways such as cell differentiation, metal ion homeostasis, pathogen virulence, redox, and universal stress responses.

RNA-seq analysis identified glucose-responsive genes and YqfO as a global regulator in Bacillus subtilis

“…As a result, we first observed that disruption of the yqfO gene has a broad impact on genome gene expression. YqfO belongs to a large protein superfamily with unknown functions (DUF34), which is conserved in all three domains of life [ 11 ]. Although an exact mechanistic analysis was lacking, pleiotropic effects on physiological aspects, including transcription regulation, were observed in the disruptants of the genes encoding DUF34 proteins in many organisms [ 11 ].…”

“…YqfO belongs to a large protein superfamily with unknown functions (DUF34), which is conserved in all three domains of life [ 11 ]. Although an exact mechanistic analysis was lacking, pleiotropic effects on physiological aspects, including transcription regulation, were observed in the disruptants of the genes encoding DUF34 proteins in many organisms [ 11 ]. The Thermus thermophilus DUF34 protein YbgI binds to single-stranded DNA [ 18 ], and the Geobacillus stearotherophilus DUF34 protein XynX regulates the xynA gene encoding xylanase through its binding to the xynA promoter [ 19 ].…”

“…The structure of Bacillus cereus YqfO has been resolved, revealing the presence of a dimetal-binding motif [ 10 ]. Recently, bioinformatics analysis using data from the determined genome sequences and published reports revealed that YqfO may function as a metal chaperone or metal insertase [ 11 ]. We observed that YqfO is under positive control of YlxR [ 8 ].…”

[Fe]‐Hydrogenase, Cofactor Biosynthesis and Engineering

“…HcgD presumably works as an iron‐trafficking protein (Figure 10). [41] HcgD belongs to the Nif3 (NGG1p‐interacting factor 3)‐like protein family, a class of metalloproteins containing a dinuclear metal center [42] . As predicted, the crystal structure of HcgD from M. jannaschii presented a dinuclear iron‐binding site (Figure 10).…”

“…If the HcgD functions as an iron‐trafficking protein, the toroid structure can dissociate with the functional dimer to interact with the partner enzyme responsible for the iron complex formation. A recent comparative genomic analysis of the Nif3 family proteins discusses about the metal ion‐insertion function [42] . However, other physiological functions of HcgD cannot be ruled out.…”