Analysis of the 5' Untranslated Region Length-Dependent Control of Gene Expression in Maize: A Case Study with the ZmLAZ1 Gene Family

Abstract

The untranslated regions (UTRs) within plant mRNAs play crucial roles in regulating gene expression and the functionality of post-translationally modified proteins by various mechanisms. These regions are vital for plants' ability to sense to multiple developmental and environmental stimuli. In this study, we conducted a genome-wide analysis of UTRs and UTR-containing genes in maize (Zea mays). Using the ZmLAZ1 family as a case study, we demonstrated that the length of 5' UTRs could influence gene expression levels by employing GUS reporter gene assays. Although maize and arabidopsis (Arabidopsis thaliana), as well as rice (Oryza sativa), have distinct functional categories of UTR-containing genes, we observed a similar lengthwise distribution of UTRs and a recurring appearance of certain gene ontology (GO) terms between maize and rice. These suggest a potentially conserved mechanism within the Poaceae species. Furthermore, the analysis of cis-acting elements in these 5' UTRs of the ZmLAZ1 gene family further supports the hypothesis that UTRs confer functional specificity to genes in a length-dependent manner. Our findings offer novel insights into the role of UTRs in maize, contributing to the broader understanding of gene expression regulation in plants.

Keywords: 5′ UTR; Lazarus 1 gene family; gene expression; maize.

Figure 1

The percentages of coding sequence (CDS) and untranslated region (UTR) elements in maize and their lengths. (A) A genome-scale survey showing the percentages of transcript bases involved in protein coding (CDS) and in gene regulation (UTR) in maize (Z. mays). (B) Percentages of 5′ and 3′ UTRs in different length categories along with the average UTR length (bp) at the whole-genome level and in orthologs.

Figure 2

Functional enrichment analysis of untranslated region (UTR)-containing genes in maize. UTR-containing genes of maize genomes were sorted according to their 5′ UTR (A) and 3′ UTR (B) lengths before functional enrichment analysis was independently performed for genes with short (1−500 bp), medium (501−1000 and 1001−2000 bp), and long (>2000 bp) UTRs. On the basis of p values, the top five GO terms related to biological processes are represented independently for 5′ and 3′ UTRs.

Figure 3

Percentages of coding sequence (CDS) and untranslated region (UTR) elements in maize (a) Schematic representation of the ZmLAZ1 gene family members with 5′ UTRs. (b) Specific fragments of the 5′ UTR sequences of the ZmLAZ1 genes cloned from the maize cDNA sample and separated by agarose gel electrophoresis.

Figure 4

GUS reporter assays. (a) Schematic diagrams of the reporters used for the GUS assay. (b) Histochemical GUS staining in tobacco leaves. The depth of color represents the different expression levels of the GUS protein. (c) GUS enzyme activity assay in tobacco leaves. Student’s t-test; **, p < 0.01; *, p < 0.05.

Figure 5

FPKM distribution of the ZmLAZ1 family members in all libraries of the PPRD database.

Figure 6

Analysis of cis-acting elements in the 5′ UTR of the ZmLAZ1 gene family. (a) The cis-acting elements of the 5′ UTR region, and different color blocks represent different elements. (b) The putative cis-elements were quantified and functionally classified based on their established roles in gene transcriptional regulation.