A tokenizer is what you want. Here's an implementation:

my $line ='"Transcription factor" promoter DNA';

my $fixed;
for ($line) {
   /\G ( \" [^"]+ \" ) /xgc && do { $fixed .= $1;  redo };
   /\G ( [^"\s]+     ) /xgc && do { $fixed .= $1;  redo };
   /\G   \s+           /xgc && do { $fixed .= ','; redo };
   last;
}

print("$fixed\n");
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